Targeted Genome Mining—From Compound Discovery to Biosynthetic Pathway Elucidation

Abstract

Natural products are an important source of novel investigational compounds in drug discovery. Especially in the field of antibiotics, Actinobacteria have been proven to be a reliable source for lead structures. The discovery of these natural products with activity- and structure-guided screenings has been impeded by the constant rediscovery of previously identified compounds. Additionally, a large discrepancy between produced natural products and biosynthetic potential in Actinobacteria, including representatives of the order Pseudonocardiales, has been revealed using genome sequencing. To turn this genomic potential into novel natural products, we used an approach including the in-silico pre-selection of unique biosynthetic gene clusters followed by their systematic heterologous expression. As a proof of concept, fifteen Saccharothrixespanaensis genomic library clones covering predicted biosynthetic gene clusters were chosen for expression in two heterologous hosts, Streptomyceslividans and Streptomycesalbus. As a result, two novel natural products, an unusual angucyclinone pentangumycin and a new type II polyketide synthase shunt product SEK90, were identified. After purification and structure elucidation, the biosynthetic pathways leading to the formation of pentangumycin and SEK90 were deduced using mutational analysis of the biosynthetic gene cluster and feeding experiments with 13C-labelled precursors.

Impact of wine-grape continuous cropping on soil enzyme activity and the composition and function of the soil microbial community in arid areas

“…With the increase of cropping years, the relative abundances of Solirubrobacterales and Pseudonocardiales showed an increasing trend. This could be attributed to Solirubrobacterales and Pseudonocardiales have extremely diverse trophic modes, which change with different soil conditions, resulting in different relative abundances ( Shange et al, 2012 ; Gummerlich et al, 2020 ).…”

Bacterial natural product discovery by heterologous expression

“…The overlapping pieces of the BGCs were then assembled into a BAC by TAR cloning and integrated into the chromosome of the hosts (Paulus et al 2022;Hover et al 2018;Wu et al 2019). Moreover, recombination methods like Red/ET can be used to introduce a selective marker (Lasch et al 2021;Lasch, Stierhof, et al 2020;Shuai et al 2020) or insert integration machinery into the vector (Gummerlich et al 2020).…”

“…The most frequent approach (56%) was to prioritize novelty by expressing unusual BGCs found in rare and/or understudied bacteria, exemplified by the discovery of the lanthipeptide marinsedin from Marinicella sedimis (Han et al 2022), and by the discovery of 31 other compounds listed in SI Table S1 (Hashimoto et al 2021;Hao et al 2019;Zhang et al 2021;Lasch et al 2021;Enghiad et al 2021;Shi et al 2019;Yuet et al 2020;De Rond, Asay, and Moore 2021;Wang et al 2023;Liu et al 2021;Lasch, Stierhof, et al 2020;Li et al 2020;Myronovskyi et al 2018;Gao et al 2023;Cheng et al 2023;Koos and Link 2019;Kaweewan, Nakagawa, and Kodani 2021;S. H. Liu et al 2019;Shuai et al 2020;Lasch, Gummerlich, et al 2020;Paulus et al 2022;Bothwell et al 2021;Gummerlich et al 2020;Alberti et al 2019;Vermeulen et al 2022;Zhang et al 2021;Unno et al 2020).…”

“…License: CC BY-NC-ND 4.0 studies. Fortuitously, four large-scale studies from which success rates can be derived were included in the 50 studies reviewed here (Table 1) (Enghiad et al 2021;Libis et al 2022;Gummerlich et al 2020;Ayikpoe et al 2022). We summarize these four studies below in chronological order of publication.…”

Integrating perspectives in actinomycete research: an ActinoBase review of 2020–21

“…The genomic era has opened a new roadmap for the study of BGCs with genome mining as a prominent strategy to find candidates for novel bioactive compounds [4,13,14]. This has allowed researchers to uncover thousands of new BGCs of different classes, including polyketides (PKs); non-ribosomal peptides (NRPs) [15][16][17][18]; PK-NRP hybrid compounds; ribosomally synthesized and post-translationally modified peptides (RiPPs) such as lanthipeptides or thiopeptides [19][20][21]; and volatile organic compounds (VOCs) [22,23]; among others [24][25][26][27][28].…”